git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/CNEr@110396 bc3139a8-67e5-0310-9ffc-ced21a209358
Ge Tan authored on 06/11/2015 13:55:36
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Package: CNEr |
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-Version: 1.6.0 |
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-Date: 2015-10-08 |
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+Version: 1.6.1 |
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+Date: 2015-11-06 |
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Title: CNE Detection and Visualization |
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Description: Large-scale identification and advanced visualization |
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of sets of conserved noncoding elements. |
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@@ -17,12 +17,13 @@ System Requirements: blat |
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VignetteBuilder: knitr |
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License: GPL-2 | file LICENSE |
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License_restricts_use: yes |
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-URL: http://ancora.genereg.net/ |
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+URL: https://bitbucket.org/ge11232002/cner |
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+BugReports: https://bitbucket.org/ge11232002/cner/issues |
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Type: Package |
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biocViews: GeneRegulation, Visualization, DataImport |
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NeedsCompilation: yes |
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LazyData: no |
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Collate: AllGenerics.R AllClasses.R utils.R ceScan.R plot.R |
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makeGeneDbFromUCSC.R io.R scoringMatrix.R subAxt-methods.R |
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- Axt-methods.R DB.R AssemblyStats.R |
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+ Axt-methods.R DB.R AssemblyStats.R GRB.R |
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new file mode 100644 |
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+ |
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+ |
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+makeGRBs <- function(x, winSize=NULL, genes=NULL, ratio=0.5){
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+ # winSize in kb |
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+ x <- unlist(x) |
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+ x <- reduce(x) |
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+ cov <- coverage(x) |
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+ |
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+ # Guess winSize from genome size if NULL |
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+ if(is.null(winSize)){
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+ ## Based on 300kb for human |
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+ winSize <- seqlengths(x) / 3e6 * 300 |
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+ } |
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+ winSize <- winSize * 1e3 |
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+ |
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+ # calculate the background percentage of coverage |
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+ coveredAll <- sum(sum(cov)) / sum(as.numeric(seqlengths(x))) |
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+ density <- runmean(cov, k=winSize, endrule="constant") |
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+ |
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+ # slice the density into GRBs |
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+ s <- slice(density, lower=coveredAll*ratio, includeLower=FALSE) |
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+ clusterRanges <- GRanges(seqnames=rep(names(s), elementLengths(s)), |
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+ ranges=unlist(ranges(s)), |
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+ strand="+", |
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+ seqinfo=seqinfo(x)) |
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+ |
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+ # remove GRBs (which do not encompass any gene) |
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+ if(!is.null(genes)){
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+ hits <- findOverlaps(genes, clusterRanges, type="within", select="all", |
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+ ignore.strand=TRUE) |
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+ indexKeep <- unique(subjectHits(hits)) |
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+ clusterRanges <- clusterRanges[indexKeep] |
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+ } |
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+ return(clusterRanges) |
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+ |
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+} |
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+ |